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  <div class="section" id="searching-for-the-tio2-001-1x4-reconstruction">
<h1>Searching for the TiO2(001)-(1x4) reconstruction<a class="headerlink" href="#searching-for-the-tio2-001-1x4-reconstruction" title="Permalink to this headline"></a></h1>
<p>For this tutorial we will use the dftb-calculator with
the tiorg parameters.</p>
<p>This tutorial is very similar to the previous one for TiO clusters,
<a class="reference internal" href="../tio_clusters/tio_clusters.html#searching-for-tio-clusters"><span class="std std-ref">searching for TiO clusters</span></a>. It is
recomended that you do that one before the present one, as it is more
detailed.</p>
<p>The major difference in the present tutorial is that the template will
now not be empty, but contain a number of atoms fixed at bulk positions.</p>
<p>The template is defined in the file <a class="reference download internal" download="" href="../../_downloads/48a3592164be1fd976d7632aba915fba/TiO2_slab.traj"><code class="xref download docutils literal notranslate"><span class="pre">TiO2_slab.traj</span></code></a>. The
following code <a class="reference download internal" download="" href="../../_downloads/19ab4ff0523b6603bbb89aab36f4db1b/TiO2.py"><code class="xref download docutils literal notranslate"><span class="pre">TiO2.py</span></code></a> is used to carry out the search:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">from</span> <span class="nn">ase.calculators.dftb</span> <span class="k">import</span> <span class="n">Dftb</span>
<span class="kn">from</span> <span class="nn">ase.io</span> <span class="k">import</span> <span class="n">read</span>

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<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
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<span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>

<span class="c1">### Define calculator ###</span>
<span class="n">calc</span> <span class="o">=</span> <span class="n">Dftb</span><span class="p">(</span><span class="n">label</span><span class="o">=</span><span class="s1">&#39;TiO2_surface&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_SCC</span><span class="o">=</span><span class="s1">&#39;No&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_MaxAngularMomentum_</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_MaxAngularMomentum_Ti</span><span class="o">=</span><span class="s1">&#39;&quot;d&quot;&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_MaxAngularMomentum_O</span><span class="o">=</span><span class="s1">&#39;&quot;p&quot;&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_Charge</span><span class="o">=</span><span class="s1">&#39;0.000000&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_Filling</span> <span class="o">=</span><span class="s1">&#39;Fermi {&#39;</span><span class="p">,</span>
            <span class="n">Hamiltonian_Filling_empty</span><span class="o">=</span> <span class="s1">&#39;Temperature [Kelvin] = 0.000000&#39;</span><span class="p">,</span>
            <span class="n">kpts</span><span class="o">=</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">1</span><span class="p">))</span>

<span class="c1">### Set up StartGenerator and mutations ###</span>
<span class="c1"># read slab</span>
<span class="n">slab</span> <span class="o">=</span> <span class="n">read</span><span class="p">(</span><span class="s1">&#39;TiO2_slab.traj&#39;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="s1">&#39;0&#39;</span><span class="p">)</span>

<span class="c1"># Stoichiometry of atoms to be placed</span>
<span class="n">stoichiometry</span> <span class="o">=</span> <span class="mi">5</span><span class="o">*</span><span class="p">[</span><span class="mi">22</span><span class="p">]</span><span class="o">+</span><span class="mi">10</span><span class="o">*</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span>

<span class="c1"># Box in which to place atoms</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">slab</span><span class="o">.</span><span class="n">get_cell</span><span class="p">()</span>
<span class="n">v</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.5</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">8.</span><span class="p">))</span>
<span class="n">box</span> <span class="o">=</span> <span class="p">[</span><span class="n">p0</span><span class="p">,</span> <span class="n">v</span><span class="p">]</span>

<span class="c1"># initialize startgenerator</span>
<span class="n">sg</span> <span class="o">=</span> <span class="n">StartGenerator</span><span class="p">(</span><span class="n">slab</span><span class="p">,</span> <span class="n">stoichiometry</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>

<span class="c1"># initialize rattle and permutation mutations</span>
<span class="n">n_to_optimize</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">stoichiometry</span><span class="p">)</span>
<span class="n">permutation</span> <span class="o">=</span> <span class="n">PermutationMutation</span><span class="p">(</span><span class="n">n_to_optimize</span><span class="p">,</span> <span class="n">Npermute</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">rattle</span> <span class="o">=</span> <span class="n">RattleMutation</span><span class="p">(</span><span class="n">n_to_optimize</span><span class="p">,</span> <span class="n">Nrattle</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">rattle_range</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>

<span class="n">candidate_generator</span> <span class="o">=</span> <span class="n">CandidateGenerator</span><span class="p">([</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">],</span>
                                         <span class="p">[</span><span class="n">sg</span><span class="p">,</span> <span class="n">permutation</span><span class="p">,</span> <span class="n">rattle</span><span class="p">])</span>

<span class="c1">### Initialize and run search ###</span>
<span class="n">search</span> <span class="o">=</span> <span class="n">GOFEE</span><span class="p">(</span><span class="n">calc</span><span class="o">=</span><span class="n">calc</span><span class="p">,</span>
               <span class="n">startgenerator</span><span class="o">=</span><span class="n">sg</span><span class="p">,</span>
               <span class="n">candidate_generator</span><span class="o">=</span><span class="n">candidate_generator</span><span class="p">,</span>
               <span class="n">max_steps</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
               <span class="n">population_size</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
<span class="n">search</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
</pre></div>
</div>
<p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
the code as:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">TiO2</span><span class="o">.</span><span class="n">py</span>
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</pre></div>
</div>
<div class="section" id="setting-up-the-system-atoms-in-template">
<h2>Setting up the system - atoms in template<a class="headerlink" href="#setting-up-the-system-atoms-in-template" title="Permalink to this headline"></a></h2>
<p>In this case the <em>template</em> contains a number of fixed atoms representing the
slap, on top of which we want to optimize a number of atoms given by
<em>stoichiometry</em>. The final thing we need to initialize the <code class="xref py py-class docutils literal notranslate"><span class="pre">StartGenerator</span></code>
, used for generation initial structures, is the <em>box</em> within which the
<code class="xref py py-class docutils literal notranslate"><span class="pre">StartGenerator</span></code> places atoms randomly.
In this case we choose a box=[p0, v] of height 2.5 starting at p0=(0,0,8), which
is slightly above the slab atoms.
To initialize the startgenerator, we first read in the template:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ase.io</span> <span class="k">import</span> <span class="n">read</span>
<span class="n">slab</span> <span class="o">=</span> <span class="n">read</span><span class="p">(</span><span class="s1">&#39;TiO2_slab.traj&#39;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="s1">&#39;0&#39;</span><span class="p">)</span>
</pre></div>
</div>
<p>then define the stoichiometry of atoms to be optimized on top of the slab,
in the form of a list of atomic numbers:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">stoichiometry</span> <span class="o">=</span> <span class="mi">5</span><span class="o">*</span><span class="p">[</span><span class="mi">22</span><span class="p">]</span><span class="o">+</span><span class="mi">10</span><span class="o">*</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span>
</pre></div>
</div>
<p>Then define the <em>box</em> within which the <code class="xref py py-class docutils literal notranslate"><span class="pre">StartGenerator</span></code> places atoms randomly:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">slab</span><span class="o">.</span><span class="n">get_cell</span><span class="p">()</span>
<span class="n">v</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.5</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">8.</span><span class="p">))</span>
<span class="n">box</span> <span class="o">=</span> <span class="p">[</span><span class="n">p0</span><span class="p">,</span> <span class="n">v</span><span class="p">]</span>
</pre></div>
</div>
<p>Finally the <code class="xref py py-class docutils literal notranslate"><span class="pre">StartGenerator</span></code> can be initialized:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">candidate_operations.candidate_generation</span> <span class="k">import</span> <span class="n">StartGenerator</span>
<span class="n">sg</span> <span class="o">=</span> <span class="n">StartGenerator</span><span class="p">(</span><span class="n">slab</span><span class="p">,</span> <span class="n">stoichiometry</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>


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